KPOCN


	An Integrative Model for Identification of Key Players of the Cancer Network

News	2016/12/21: Source codes and data sets are updated..
Introduction	KPOKN identifies the key genes whose alterations cause dramatic effects on the activation of Multi Type Interaction Gene Network It integrates matched copy number and gene expression data, and PPI network to construct a large scale gene network with multiple interactions then, a majority scoring function is proposed to measure the effect of each gene throughout the network.
Paper	Amgalan, B. Tseveendorj, I and Lee, H. (2016) Key players on cancer-activated multi-type interaction network
Source codes	Source codes were implemented in MatLab and are available here (use KPOCN Souce Code) . Instructions for running source codes are here (use ReadMe File). The source codes require six input files such as Cancer and Normal copy number and gene expression samples in matrix forms, PPI network as a list of interactions and a list of genes for the analysis. Input files for breast cancer data can be downloaded from here (use Breast Cancer Data). Note that source codes and input files should be located in same folder.
Data sets	The breast cancer data sets used in the experiments were collected from TCGA(Use https://cancergenome.nih.gov/). Protein-protein interaction data sets were collected from the Human Protein Reference Database HPRD(Prasad et al.,2009)(Use http://www.hprd.org/) consisting of a list of interactions in the PPI network.
Contacts	bayarbaatar at seas.num.edu.mn, hyunjulee at gist.ac.kr

An Integrative Model for Identification of Key Players of the Cancer Network

News

2016/12/21: Source codes and data sets are updated..

Introduction

KPOKN identifies the key genes whose alterations cause dramatic effects on the activation of Multi Type Interaction Gene Network It integrates matched copy number and gene expression data, and PPI network to construct a large scale gene network with multiple interactions then, a majority scoring function is proposed to measure the effect of each gene throughout the network.

Paper

Amgalan, B. Tseveendorj, I and Lee, H. (2016) Key players on cancer-activated multi-type interaction network

Source codes

Source codes were implemented in MatLab and are available here (use KPOCN Souce Code) . Instructions for running source codes are here (use ReadMe File). The source codes require six input files such as Cancer and Normal copy number and gene expression samples in matrix forms, PPI network as a list of interactions and a list of genes for the analysis. Input files for breast cancer data can be downloaded from here (use Breast Cancer Data). Note that source codes and input files should be located in same folder.

Data sets

The breast cancer data sets used in the experiments were collected from TCGA(Use https://cancergenome.nih.gov/). Protein-protein interaction data sets were collected from the Human Protein Reference Database HPRD(Prasad et al.,2009)(Use http://www.hprd.org/) consisting of a list of interactions in the PPI network.

Contacts

bayarbaatar at seas.num.edu.mn, hyunjulee at gist.ac.kr